You can get about as scientific and serious about the acoustical harmonics and aereodynamics of your fipple and optimal hole size and placement as you want to; just go to some of the links on Chiff & Fipple and away you go. The only thing to be aware of is that getting really serious can result in not having nearly as much fun.

Even if you do realize perfect pitch, intonation, and interval, just pop it up to the next octave or "register", and watch the whole thing fly right out the window! This happens with the fife as well; we kind of have to decide which register we are going to play in most of the time and get an instrument tuned accordingly. It helps if the whole Corps has the same brand and style of instrument, as their idiosyncracies are at least compatable and they do not "fight" with each other as dissimmilar instruments are apt to do. I have one fife for loud, shrill "Military" use, and another for dirges and slow airs.
To a certain extent, you can compensate for some of these quirks as has been suggested, by alternate fingerings or breath delivery.
About the only time I worry about being sort-of in tune (like the man sez; this ain't Carnagie Hall) is when trying to mix with other Musicians; then it is nice to have 2 or 3 whistles in various keys. The "Pros" sometimes use the high-end tunables here, but quite a few of them still use off-the-shelf Clarkes and Generations etc. and do remarkably well with them in spite of all the rocket science.
If a whistle sounds good to you and most listeners and you have fun playing it, I'd suggest leaving the tuner in the guitar case and just ENJOY!!!